Genome Structure in Reptiles

Isochores are large regions of a genome that have a homogeneous nucleotide composition. Prominent in mammals and birds, we have shown that GC-rich isochores are entirely absent from the Anolis lizard (Fujita et al. 2011; Alfodi et al. 2011); in contrast, the compositional variation of other lizards, crocodilians, and turtles are intermediate between Anolis and mammals (Shaffer et al. 2013; Castoe et al. 2013; Greene et al. 2014; Georges et al. 2015), highlighting the incredible diversity of genome structures in reptiles that is not seen in mammals and birds. This is why our lab strongly believes that reptiles are important systems to understand genome dynamics and evolution. Given continuing advances and affordability of genome sequencing, especially long-read and haplotype sequencing, it is now feasible to use population-scale sequencing of non-model organisms, such as reptiles, to better understand the evolutionary processes that influence base composition (including recombination and mutation).

My lab will is also embarking on a novel research trajectory to analyze genome structure by borrowing from the strong theoretical foundations of ecology. Ecology aims to describe the distribution and abundance of individuals over a landscape, and in many ways genomes are “landscapes” where genes, isochores, repetitive elements, and even nucleotides are the individual entities. Starting with diversity indices that consider both species richness and abundance to measure the evenness of the distributions of different genomic entities, we will continue to develop more advanced models that incorporate genomic interactions (for example, competition for resources such as particular genomic locations). While this perspective of genome structure and function has some foundation (e.g. selfish genetic elements), my lab will explicitly incorporate ecological theory to impart novel insight into genome structure and function by describing the distribution and abundance of genomic entities.

Histogram of isochores showing the greater diversity in dog compared to Anolis lizard. This is exemplified by calculating Simpson’s index of isochores (based on GC content “species”): Anolis has fewer and less abundant isochores than dog.

If you are thinking about graduate school and are interested in studying evolutionary genomics, please contact me!

Fujita, M. K., S. V. Edwards, and C. P. Ponting. 2011. The Anolis lizard genome: an amniote genome without isochores. Genome Biology and Evolution 3:974-984.

Alfoldi et al. 2011. The genome of Anolis carolinensis, the green anole lizard, and a comparative analysis with birds and mammals.  Nature 477:587-591.

Shaffer, H. B. et al. 2013. The Painted turtle genome: extreme physiological adaptations in a slowly evolving lineage. Genome Biology 14:R28.

Castoe, T. A., et al. 2013. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences USA 110(51):20645-20650.

Greene, R.E. et al. 2014. The genomes of three crocodilians provide insight into Archosaur evolution. Science 346: 1254449

Georges, A. et al. 2015.  High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps. GigaScience, 4(1), 45.